Showing papers on "Molecular models of DNA published in 1986"
TL;DR: An extensive investigation involving as variable parameters the length of the DNA specimen, the amount of condensed counterion charge, and the geometrical parameters identifying the local opening has shown that the proposed transcription mechanism is reasonable, and that the DNA model considered here may fill a gap between accurate models including all the interactions—and employed at present for small fragments—and unstructured models addressed to inspect the behavior at the limit of infinite DNA length.
Abstract: A very simple model of DNA in biological media, consisting of electric charges related to the phosphate groups and to counterions immersed in structured media of constant permittivity, is introduced and tested with the study of a model for the first stages of the DNA transcription.
This process is modeled into two steps involving three ‘states’: (1) the DNA system at the equilibrium, (2) the DNA with a small portion deprived of counterions, and (3) the DNA with a partial opening of the double helix in correspondence of the zone deprived of counterions.
An extensive investigation involving as variable parameters the length of the DNA specimen (from 31 to 1511 base pairs), the amount of condensed counterion charge (from complete compensation to zero), and the geometrical parameters identifying the local opening has shown that the proposed transcription mechanism is reasonable, and that the DNA model considered here may fill a gap between accurate models including all the interactions—and employed at present for small fragments—and unstructured models addressed to inspect the behavior at the limit of infinite DNA length.
23 citations
TL;DR: It is shown that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules, and the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics.
Abstract: We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.
14 citations